Conformational ensembles explored dynamically from disordered peptides targeting chemokine receptor CXCR4

Abstract

This work reports on the design andthe synthesis of two short linear peptides both containing a few amino acids with disorder propensity and an allylic ester group at the  C-terminal end. Their structural properties were firstly analyzed by means of experimental techniques in solution such as CD and NMR methodsthat highlighted peptide flexibility. These results were further confirmed by MD simulationsthat demonstrated the ability of the peptides to assume conformational ensembles. Theyrevealed a network of transient and dynamic -bonds and interactions with water molecules. Binding assays with a well-known drug-target, i.e., the CXCR4 receptor, were also carried out in an attempt to verify their biological function and the possibility to use the assays to develop new specific targets for CXCR4. Moreover, our data indicate that these peptides represent useful tools for molecular recognition processes in which a flexible conformation is required in order to obtain an interaction with a specific target.